U.S. Secretary of State John Kerry speaks in Geneva on Sept. 12, 2013. / Larry Downing, AP

by Jim Michaels , USA TODAY

by Jim Michaels , USA TODAY

Identifying and eliminating Syria's chemical weapons stockpiles while the country is enmeshed in a civil war is an unprecedented challenge, made even riskier by rebel groups who may oppose the effort, analysts say.

"There has never been an effort to disarm an entire country of its chemical weapons during a civil war," said Gregory Koblentz, a professor at George Mason University who specializes in weapons of mass destruction.

The United States and Russia reached an agreement over the weekend to eliminate Syria's chemical weapons.

In Jerusalem on Sunday, U.S. Secretary of State John Kerry briefed Israeli leaders on the agreement and said military options against Syria were still available. "The threat of force is real, and the Assad regime and all those taking part need to understand that President Obama and the United States are committed to achieve this goal," he said.

Meanwhile a high-ranking Syrian official called the U.S.-Russian agreement on securing Syria's chemical weapons a "victory" for President Bashar Assad's regime, The comments by Syrian Minister of National Reconciliation Ali Haidar to a Russian state news agency were the first by a senior Syrian government official on the deal.

"We welcome these agreements," Haidar was quoted as saying by the RIA Novosti agency. "On the one hand, they will help Syrians get out of the crisis, and on the other hand, they averted a war against Syria by removing the pretext for those who wanted to unleash one."

Details of how the agreement will work have yet to be worked out. Ultimately, the effort will be under the authority of a United Nations resolution and carried out by the international organization responsible for the international chemical weapons ban.

Historically, eliminating chemical weapons programs take years, even when a regime is fully cooperative. After Libyan leader Moammar Gadhafi agreed to relinquish his weapons of mass destruction it took a decade to remove its chemical stockpiles. Most of that was accomplished during peacetime.

Syria's situation is far more complex. Aside from the widespread violence tearing apart the country is the question of whether rebels will even cooperate.

"The rebels are angry, but it doesn't change the fundamental military balance on the ground," said Jeffrey White, an analyst at the Washington Institute for Near East Policy and a former Defense Intelligence Agency official.

But rebels may have cause for concern as the process moves forward, heightening their suspicions of the U.S.-Russian agreement.

White said that if the United States pursues a broader agreement to end the fighting, Washington could place pressure on the rebels to tamp down military operations. "That shows we could get sucked into the business of pressuring the rebels to do less in the hopes of getting a negotiated settlement," he said.

Rebel groups could try to impede inspectors if they feel the agreement is not in their interests. "They could take pot shots at them," White said. The opposition in Syria consists of a variety of factions, including radical Islamists, who don't always cooperate or fall under a unified command.

When inspectors came to examine evidence of the Aug. 21 chemical attack near Damascus, which triggered the latest crisis, they were fired upon, though no one was injured and it was not clear who was responsible for the attack.

It's possible rebel cooperation won't be essential. The State Department believes all the chemical weapons are in the hands of Assad's regime, suggesting that the regime could provide much of the security for inspectors. If inspectors need to stray into rebel control areas, opposition forces, however, might be asked to provide safe passage, White said.

The agreement also calls on the foreign community to support and assist the process of removing chemical weapons, some of whom could be called on to help with security.

The State Department believes there are 45 sites associated with Assad's chemical weapons programs. They believe Assad's military has about 1,000 metric tons of deadly chemicals, including nerve agents and mustard gas.

In the past, the Pentagon has said Assad's forces have moved the chemical weapons around in an effort to keep the stocks from being captured by rebel forces.

The security challenges are set against an unprecedented pace for eliminating the chemicals.

Under the agreement, Assad's regime needs to turn over a complete list of chemical stockpiles and production facilities within a week. The agreement calls for completely eliminating its chemical weapons in less than a year.

Traditionally, chemical weapons have been destroyed on premises, a lengthy process because of the difficulty in handling highly toxic chemicals.

The U.S-Russian agreement makes provisions for removing the weapons and shipping them outside Syria for destruction, which could expedite the process, Koblentz said. Still, that might require moving dangerous chemicals through unstable regions of the country.

"Their odds of doing it on time are not very good," White said. But, he said, if progress is being made and all parties are acting in good faith, delays will not be a problem.